rxiv-maker 1.16.4__py3-none-any.whl → 1.16.5__py3-none-any.whl

rxiv_maker/__version__.py

@@ -1,3 +1,3 @@
 """Version information."""
 
-__version__ = "1.16.4"
+__version__ = "1.16.5"

rxiv_maker/cli/commands/upgrade.py

@@ -1,9 +1,10 @@
 """Upgrade command for rxiv-maker CLI."""
 
+import subprocess  # nosec B404 - needed for executing upgrade commands
 import sys
 
 import click
-from henriqueslab_updater import execute_upgrade, force_update_check
+from henriqueslab_updater import force_update_check
 from rich.console import Console
 
 from ... import __version__
@@ -119,11 +120,32 @@ def upgrade(ctx: click.Context, yes: bool, check_only: bool) -> None:
             console.print("❌ Upgrade cancelled", style="yellow")
             sys.exit(0)
 
-    # Execute upgrade command using centralized executor
+    # Execute upgrade command directly
     console.print("\n🚀 Upgrading rxiv-maker...", style="blue")
     console.print(f"   Running: {upgrade_cmd}", style="dim")
 
-    success, error = execute_upgrade(upgrade_cmd, show_output=True, timeout=300)
+    try:
+        # Split command for safer execution without shell=True
+        import shlex
+
+        cmd_parts = shlex.split(upgrade_cmd)
+        result = subprocess.run(
+            cmd_parts,
+            check=True,
+            capture_output=False,
+            timeout=300,
+        )  # nosec B603 - upgrade_cmd comes from trusted install_detector module
+        success = result.returncode == 0
+        error = None
+    except subprocess.CalledProcessError as e:
+        success = False
+        error = f"Command failed with exit code {e.returncode}"
+    except subprocess.TimeoutExpired:
+        success = False
+        error = "Upgrade timed out after 5 minutes"
+    except Exception as e:
+        success = False
+        error = str(e)
 
     if success:
         console.print("\n✅ Upgrade completed successfully!", style="green")

rxiv_maker/templates/registry.py

@@ -163,38 +163,36 @@ citation_style: "numbered"
         """Get default main manuscript template."""
         return """## Abstract
 
-Your manuscript abstract goes here. Provide a comprehensive summary of your work,
-key findings, and significance to the field.
+Your manuscript abstract goes here. Provide a comprehensive summary of your work, including the main problem you are addressing, your approach, key findings, and the significance of your results to the field. The abstract should be self-contained and provide readers with a clear understanding of your contribution. Aim for 150-300 words that capture the essence of your research.
 
 ## Introduction
 
-Introduce your topic, provide background, and state your objectives.
+Introduce your research topic by providing essential background context and motivation. Start with the broader significance of your field, then narrow down to the specific problem your work addresses. Clearly state your research objectives and how your approach differs from or builds upon existing work in the literature [@smith2023]. Explain why this research is important and what gap in knowledge it fills.
 
 ## Methods
 
-Describe your methods, approaches, and techniques.
-(For reviews, you can remove this section or describe your literature search strategy)
+Describe your experimental design, data collection procedures, and analytical techniques in sufficient detail to allow replication of your work. For computational studies, specify software versions, parameters, and algorithms used. For experimental work, detail protocols, sample preparation, and measurement procedures [@johnson2022]. Include information about statistical methods and data validation approaches. If you are writing a review article, you may remove this section or describe your literature search and selection strategy.
 
 ## Results
 
-Present your findings with supporting figures and tables.
-(For reviews, you can remove this section or rename it to organize your discussion)
+Present your findings in a logical sequence, using figures and tables to support your narrative. Start with an overview of the key results, then provide detailed analyses.
 
-![](FIGURES/Figure__example.mmd)
-{{#fig:example}} **Example Figure.** This is an example Mermaid diagram that will be automatically converted to PDF during build.
+![A flowchart showing the progression from data input through processing to results output](FIGURES/Figure__example.mmd)
+{{#fig:example}} **Example workflow diagram.** This Mermaid diagram illustrates a typical data processing pipeline, automatically converted to PDF during manuscript compilation. The diagram shows three stages: data input (gray), processing and analysis (red), and results output (green).
+
+Our analysis demonstrates that the methodology produces consistent results across different datasets. The workflow presented in @fig:example provides a schematic overview of the processing pipeline. These findings build upon previous work [@smith2023; @johnson2022] while introducing novel approaches to data analysis.
 
 ## Discussion
 
-Interpret your findings, discuss implications, and acknowledge limitations.
+Interpret your results in the context of existing literature and theory. Discuss how your findings support or challenge current understanding in the field. Address the implications of your work for theory, practice, or policy. Acknowledge limitations of your study, such as sample size constraints, methodological limitations, or scope boundaries. Suggest directions for future research that build upon your findings.
 
 ## Conclusions
 
-Summarize your key conclusions and broader impact.
+Summarize your key findings and their significance. Reinforce the main contributions of your work and their broader impact on the field. Keep this section concise but impactful, leaving readers with a clear understanding of what your research has accomplished and why it matters.
 
 ## References
 
-Citations will be automatically formatted. Add entries to 03_REFERENCES.bib and
-reference them in your text: [@smith2023; @johnson2022]
+Citations are automatically formatted from 03_REFERENCES.bib. Reference works using citation keys like [@smith2023] for single citations or [@smith2023; @johnson2022] for multiple citations.
 """
 
     def _get_default_supplementary_template(self) -> str:
@@ -225,34 +223,60 @@ Information about code repositories, data availability, and reproducibility reso
     def _get_default_bibliography_template(self) -> str:
         """Get default bibliography template."""
         return """@article{{smith2023,
-    title = {{Example Research Article}},
-    author = {{Smith, John and Doe, Jane}},
-    journal = {{Nature}},
-    volume = {{123}},
-    pages = {{456-789}},
+    title = {{Advances in computational biology: methods and applications}},
+    author = {{Smith, John A. and Doe, Jane M. and Williams, Robert L.}},
+    journal = {{Nature Methods}},
+    volume = {{20}},
+    number = {{8}},
+    pages = {{1234--1245}},
     year = {{2023}},
-    doi = {{10.1038/nature12345}}
+    publisher = {{Springer Nature}},
+    doi = {{10.1038/s41592-023-01234-5}}
 }}
 
 @article{{johnson2022,
-    title = {{Another Important Study}},
-    author = {{Johnson, Alice and Brown, Bob}},
+    title = {{Machine learning approaches for biological data analysis}},
+    author = {{Johnson, Alice B. and Brown, Robert C. and Davis, Sarah K.}},
     journal = {{Cell}},
     volume = {{185}},
-    pages = {{1234-1245}},
+    number = {{12}},
+    pages = {{2156--2170}},
     year = {{2022}},
-    doi = {{10.1016/j.cell.2022.01.001}}
+    publisher = {{Elsevier}},
+    doi = {{10.1016/j.cell.2022.05.015}}
+}}
+
+@article{{wilson2024,
+    title = {{Reproducible research practices in modern science}},
+    author = {{Wilson, Greg and Jones, Emily R.}},
+    journal = {{PLOS Computational Biology}},
+    volume = {{20}},
+    number = {{3}},
+    pages = {{e1011234}},
+    year = {{2024}},
+    publisher = {{Public Library of Science}},
+    doi = {{10.1371/journal.pcbi.1011234}}
 }}
 """
 
     def _get_default_figure_template(self) -> str:
         """Get default figure template (Mermaid diagram)."""
-        return """graph TD
-    A[Start] --> B{{Decision}}
-    B -->|Yes| C[Process 1]
-    B -->|No| D[Process 2]
-    C --> E[End]
-    D --> E
+        return """---
+config:
+  look: neo
+  theme: neo
+---
+flowchart LR
+    A["<b>DATA</b><br/>Input"] --> B["<b>PROCESSING</b><br/>Analysis"]
+    B --> C["<b>RESULTS</b><br/>Output"]
+
+    classDef inputStyle fill:#1f2937,stroke:#374151,stroke-width:3px,color:#ffffff
+    classDef processStyle fill:#dc2626,stroke:#991b1b,stroke-width:3px,color:#ffffff
+    classDef outputStyle fill:#059669,stroke:#047857,stroke-width:3px,color:#ffffff
+
+    class A inputStyle
+    class B processStyle
+    class C outputStyle
 """
 
     def _get_default_gitignore_template(self) -> str:

{rxiv_maker-1.16.4.dist-info → rxiv_maker-1.16.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rxiv-maker
-Version: 1.16.4
+Version: 1.16.5
 Summary: Write scientific preprints in Markdown. Generate publication-ready PDFs efficiently.
 Project-URL: Homepage, https://github.com/HenriquesLab/rxiv-maker
 Project-URL: Documentation, https://github.com/HenriquesLab/rxiv-maker#readme

{rxiv_maker-1.16.4.dist-info → rxiv_maker-1.16.5.dist-info}/RECORD

@@ -1,5 +1,5 @@
 rxiv_maker/__init__.py,sha256=p04JYC5ZhP6dLXkoWVlKNyiRvsDE1a4C88f9q4xO3tA,3268
-rxiv_maker/__version__.py,sha256=9jjbeowk49aKHUW-4TiyTbFpmPEuycMrStL-jO4XzP8,51
+rxiv_maker/__version__.py,sha256=scH9t8S4Yy0pZ0rKdWKP1B1m1lQmPo9FwrixAZxLlR0,51
 rxiv_maker/rxiv_maker_cli.py,sha256=9Lu_mhFPXwx5jzAR6StCNxwCm_fkmP5qiOYdNuh_AwI,120
 rxiv_maker/validate.py,sha256=AIzgP59KbCQJqC9WIGfUdVv0xI6ud9g1fFznQkaGz5Q,9373
 rxiv_maker/cli/__init__.py,sha256=Jw0DTFUSofN-02xpVrt1UUzRcgH5NNd-GPNidhmNwpU,77
@@ -29,7 +29,7 @@ rxiv_maker/cli/commands/repos.py,sha256=SQ9nuhSkyHKFPYn_TrOxyQoGdDRI-OBOgUSGJpRu
 rxiv_maker/cli/commands/repos_search.py,sha256=6sUMvyHlHEX1p88hPtu0_Hf8z6JpOinJ53l9ZI-rirc,7743
 rxiv_maker/cli/commands/setup.py,sha256=9ue4bDETpSPGVkWFDfpuTDsysax5-QKGxmt42Gb7oeU,2294
 rxiv_maker/cli/commands/track_changes.py,sha256=omf_77A7htRSa8naUEPTTtUTxrSwMpzHFOuU0j1xAJw,1163
-rxiv_maker/cli/commands/upgrade.py,sha256=Cn2559onuCPLjqSnNDaWzS_40sPwpnRU_RLEZW5Xk4Y,5649
+rxiv_maker/cli/commands/upgrade.py,sha256=VJ1snYyLGrb5-snF4olfsMwfQsuKkAbXEr8aQ88WYYE,6349
 rxiv_maker/cli/commands/validate.py,sha256=3JghFQevJvQDQII4p_QWbQXMEUyDpM-t9-WxtaT4edo,1629
 rxiv_maker/cli/commands/version.py,sha256=VMlfSxxsrZH02d24MXLUDZfHBW39yZRpWxUpMhQ-X0Y,2737
 rxiv_maker/cli/framework/__init__.py,sha256=4FPXdP8J6v4eeEn46mwY0VtnwxjR1jnW_kTrXykQlQs,2704
@@ -141,7 +141,7 @@ rxiv_maker/services/publication_service.py,sha256=0p8yQ1jrY3RHwCkzTEl_sAbWYTafRk
 rxiv_maker/services/validation_service.py,sha256=eWg14NqJu6LzyJBgeXkTaVZAlX4wYFX8ZEvSR5hMx7U,14619
 rxiv_maker/templates/__init__.py,sha256=UTet1pYPkPdgvrLw-wwaY-PAgdjGJasAi_hdyIh0J8s,562
 rxiv_maker/templates/manager.py,sha256=HlI7Qb52866Okf4k1aRh0fUy9heOSNGjMQJtrCdL3Xk,6131
-rxiv_maker/templates/registry.py,sha256=L8M7M9Yhf2P0SQEghmCXufWfsGQhaW1TYjdkUw-wvDw,12993
+rxiv_maker/templates/registry.py,sha256=mRKUhuNg1VWzryEV-l6tD2pmdQG6b_JDh3_jtrR_K48,16200
 rxiv_maker/tex/python_execution_section.tex,sha256=pHz6NGfZN4ViBo6rInUO5FAuk81sV_Ppqszrvl00w_4,2218
 rxiv_maker/utils/__init__.py,sha256=4ya5VR8jqRqUChlnUeMeeetOuWV-gIvjPwcE1u_1OnI,1540
 rxiv_maker/utils/author_name_formatter.py,sha256=UjvarbyQm89EUIYqckygx3g37o-EcNyvipBtY8GJDxs,10222
@@ -187,8 +187,8 @@ rxiv_maker/validators/doi/metadata_comparator.py,sha256=euqHhKP5sHQAdZbdoAahUn6Y
 rxiv_maker/tex/template.tex,sha256=zrJ3aFfu8j9zkg1l375eE9w-j42P3rz16wMD3dSgi1I,1354
 rxiv_maker/tex/style/rxiv_maker_style.bst,sha256=jbVqrJgAm6F88cow5vtZuPBwwmlcYykclTm8RvZIo6Y,24281
 rxiv_maker/tex/style/rxiv_maker_style.cls,sha256=F2qtnS9mI6SwOIaVH76egXZkB2_GzbH4gCTG_ZcfCDQ,24253
-rxiv_maker-1.16.4.dist-info/METADATA,sha256=aEslQxuVrwfw0lXsEVzJTwxA_4vfAm6OrADsnYMhdAU,17950
-rxiv_maker-1.16.4.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-rxiv_maker-1.16.4.dist-info/entry_points.txt,sha256=ghCN0hI9A1GlG7QY5F6E-xYPflA8CyS4B6bTQ1YLop0,97
-rxiv_maker-1.16.4.dist-info/licenses/LICENSE,sha256=GSZFoPIhWDNJEtSHTQ5dnELN38zFwRiQO2antBezGQk,1093
-rxiv_maker-1.16.4.dist-info/RECORD,,
+rxiv_maker-1.16.5.dist-info/METADATA,sha256=2U4BcFzbnYaEhzXTOgtUCk13H5w_J_RyoCZ5lQQjaGE,17950
+rxiv_maker-1.16.5.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+rxiv_maker-1.16.5.dist-info/entry_points.txt,sha256=ghCN0hI9A1GlG7QY5F6E-xYPflA8CyS4B6bTQ1YLop0,97
+rxiv_maker-1.16.5.dist-info/licenses/LICENSE,sha256=GSZFoPIhWDNJEtSHTQ5dnELN38zFwRiQO2antBezGQk,1093
+rxiv_maker-1.16.5.dist-info/RECORD,,